[gmx-users] Gromacs-mpi with Rocks v4.0

[Arneh Babakhani]

Hi Francisco, was wondering if you ever resolved this issue?  I too am 
trying to install gromacs mpi on our cluster, but have had no luck.  I 
get the following error in the configure step:

[ababakha at chemcca40 gromacs-3.3.1]$ ./configure --enable-mpi 
--prefix=/home/ababakha/gromacs-3.3.1
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking for cc... cc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of cc... gcc3
checking for mpxlc... no
checking for mpicc... mpicc
checking whether the MPI cc command works... yes
checking how to run the C preprocessor... mpicc -E
checking whether mpicc accepts -O3... yes
checking whether mpicc accepts -malign-double... yes
checking whether mpicc accepts -funroll-all-loops... yes
checking whether mpicc accepts  -O3 -fomit-frame-pointer 
-finline-functions -Wall -Wno-unused -malign-double 
-funroll-all-loops... yes
checking whether byte ordering is bigendian... no
checking for egrep... grep -E
checking for ANSI C header files... no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for int... yes
checking size of int... configure: error: cannot compute sizeof (int), 77
See `config.log' for more details.
[ababakha at chemcca40 gromacs-3.3.1]$





Francisco Tufró wrote:
> well, i have installed the rpm versions of gromacs, and gromacs-mpi, 
> didn't compiled it by hand.
> i just wonder if there is an example of using gromacs with mpi, like 
> the demo in /usr/share/gromacs/tutor/demo but showing the usage with mpi.
> Thanks
>
> On 6/12/06, *kobi* <kobi17 at gmx.de <mailto:kobi17 at gmx.de>> wrote:
>
>     Oh, thanks for correction. I'm sorry I got the exact details wrong.
>     Didn't want to confuse anyone.
>
>     Jan
>
>     Mark Abraham schrieb:
>     > kobi wrote:
>     >> Hi Francisco
>     >>
>     >> If you intalled gromacs-mpi directly, then try to use just
>     mdrun instead
>     >> of mdrun_mpi. Normally you only have a mdrun_mpi if the
>     >> singleprocessorversion was installed first and you only added the
>     >> multiprocessorversion afterwards.
>     >
>     > Not strictly true. You need mdrun_mpi for MPI mdrun if you used the
>     > combination of --enable-mpi and --program-suffix=_mpi as recommended
>     > in the gromacs webpage installation guide. If you used only the
>     former
>     > then obvously mdrun_mpi will not be found. If you used only the
>     > latter, then that name would refer to a single-processor version(!)
>     >
>     > It is not the fact of installing a single processor version followed
>     > by a multiprocessor version that creates the naming difference,
>     it is
>     > the use of the --program-suffix directive, which you want to use to
>     > avoid name clashes. Simply doing a configure with the above
>     directives
>     > and then just "make install-mdrun" makes a stand-alone MPI mdrun
>     > perfectly.
>     >
>     > Mark
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